Theses and Dissertations from UMD
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Item Ultracold Gases in a Two-Frequency Breathing Lattice(2024) Dewan, Aftaab; Rolston, Steven L; Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Driven systems have been of particular interest in the field of ultracold atomic gases. Theprecise control and relative purity allows for construction of many novel Hamiltonians. One such system is the ‘breathing’ lattice, where both the frequency and amplitude is modulated in time, much like an accordion. We present the results of a phenomenological investigation of a proposed experiment, one where we apply a two-frequency breathing lattice to an atomic system. The results are surprising, as they indicate the possibility of a phase-dependent transition between nearest-neighbour and beyond nearest-neighbour interactions.Item A UNITED-ATOM REPRESENTATION FOR SPHINGOLIPIDS IN THE CHARMM MOLECULAR DYNAMICS FORCE FIELD(2023) Lucker, Joshua; Klauda, Jeffery B; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The development of the CHARMM force field (FF) in the late 1970’s and early 1980’s was groundbreaking at the time. For the first time, a computer program was created that could simulate biological systems on a macromolecular scale. Starting with the simulation of simple proteins, CHARMM has since expanded to include such macromolecules as nucleic acids and lipids, now being able to model complex biological systems and processes. Force fields like CHARMM can be represented in different ways. For example, force fields can be represented through an all-atom representation, in which all atoms in a system are modeled as distinct interaction units. This representation can be simplified into a united-atom representation, which shall be the primary focus of this thesis. A united atom FF has no explicit interaction sites for hydrogen. Instead, the hydrogens are lumped onto the atoms they are connected to, termed ‘heavy atoms’ as these atoms have a greater atomic weight than hydrogen. The CHARMM FF originally had a united-atom representation for proteins, which was abandoned to focus on all-atom representations. However, in certain cases, such as lipid tails, united-atom representations are often useful in certain situations; as compared to all-atom representations, united-atom models often speed up simulation times, which is useful in the simulation of large enough systems of molecules. Although there are currently united-atom representations for many types of biomolecules in the CHARMM FF, including multiple types of membrane lipids, there has yet to be a united-atom model for sphingolipids, a type of membrane lipid most commonly found in the myelin sheath of neurons, although its presence has been noted in many types of eukaryotic cells. The goal of this thesis is thus to develop such a model and implement it in the CHARMM FF.Item MOLECULAR-SCALE EXPLORATION OF INTERACTIONS BETWEEN DROPS AND PARTICLES WITH A POLYMERIC LAYER(2023) Etha, Sai Ankit; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Surface-grafted polymer molecules have been extensively employed for surface modifications as they ensure changes to the inherent physical/chemical properties of surface. Bottom-up surface processing with well-defined polymeric structures becomes increasingly important in many current technologies. Polymer brushes, which are polymer molecules grafted to a substrate by its one end at close enough proximity (thereby ensuring that they stretch out like the “bristles” of a toothbrush), provide an exemplary system of materials capable of achieving such a goal. In particular, producing functional polymer brushes with well-defined chemical configurations, densities, architectures, and thicknesses on a material surface has become increasingly important in many fields. In my dissertation, I employ Molecular Dynamics (MD) simulations to study the interplay of interactions between nanoparticles (NPs), solvent drops and polymer grafted surfaces under various system conditions. This study will help us to understand (1) the wetting dynamics of brush grafted surfaces and the associated brush conformational changes, (2) polymer-insoluble solvophilic NP assembly in brush grafted surfaces and the steric interactions driven establishment of direct contacts between a NP and a polymer layer (highly phobic to the NP), and (3) microphase separation and distillation-like behavior of grafted polymer bilayers interacting with a binary liquid mixture, and the resulting nanofluidic valving behavior of swollen polymer bilayers in a weak interpenetration regime. In Chapter 1, I provide the background and motivation of the research presented in this thesis. In Chapter 2, I study the spreading and imbibition of a liquid drop on a porous, soft, solvophilic, and responsive surface represented by a layer of polymer molecules grafted on a solvophilic solid. These polymer molecules are in a crumpled and collapsed globule-like state before the interaction with the drop, but transition to a “brush”-like state as they get wetted by the liquid drop. We hypothesize that for a wide range of densities of polymer grafting (σg), the drop spreading is dictated by the balance of the driving inertial pressure and balancing viscoelastic dissipation, associated with the spreading of the liquid drop on the polymer layer that undergoes globule-to-brush transition and serves as the viscoelastic solid. Finally, I argue that these simulations raise the possibility of designing soft and “responsive” and widely deployable liquid-infused surfaces where the polymer grafted solid, with the polymer undergoing a globule-to-brush transition, serving as the responsive “surface”. In Chapter 3, I employ coarse-grained molecular dynamics (MD) simulations and establish that under appropriate conditions, it is possible to develop numerous stable direct contacts between a polymer-insoluble NP and a solvated polymer layer (the polymer layer is phobic to the NP, while the solvent/liquid is philic to both the NP and the polymer). The NP is driven inside a layer of collapsed and phobic (to the NP) polymer molecules by a drop of this liquid (which is philic to both the NP and the polymer layer). The liquid molecules imbibe and diffuse inside the polymer layer, but the NP remains localized within the polymer layer, due to large Steric effects, ensuring the establishment of highly stable numerous direct contacts between the NP and the highly phobic polymer molecules. Finally, I argue that our finding will open up avenues for leveraging NP-polymer interactions for a myriad of applications even for cases where the polymer molecules are phobic to the NPs. In Chapter 4, I study the interaction of a binary mixture drop, containing two-miscible-liquids, with a polymer functionalized nanochannel that is philic to one of the liquids and phobic to the other. Liquid-liquid phase separation is achieved due to the asymmetry of interaction of the liquid species and we observe distillation like behavior wherein the drop becomes progressively concentrated with the phobic liquid with each ‘“pass” with the polymer bilayer absorbing an increasing fraction of the philic liquid molecules and transitioning into the polymer brush regime. Depending on the nanochannel height, the number of allowed passes varies, as the polymer chains stretch out until the oppositely grafted layers overlap and create a dense region of liquid infused polymer layers that act as a valve. Any further passage of drops through this nano-confined interpenetrating brush bilayer requires a much greater magnitude of applied force on the drop. I finally propose a design of nanovalves based on this mechanism of creating partially porous interpenetrating polymer brush layers.Item WATER, ION, AND GRAPHENE: AN ODYSSEY THROUGH THE MOLECULAR SIMULATIONS(2019) Wang, Yanbin; Das, Siddhartha; Mechanical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Water is known as the most common and complicated liquid on earth. Meanwhile, graphene, defined as single/few layer graphite, is the first member in the 2-dimensional materials family and has emerged as a magic material. Interactions between water and graphene generate many interesting phenomena and applications. This thesis focuses on applying molecular dynamics (MD), a powerful computational tool, for investigating the graphene-water interactions associated with various energetic and environmental applications, ranging from the wettability modification, species adsorption, and nanofluidic transport to seawater desalination. A key component of one domain of applications involves a third component, namely salt ions. This thesis attempts that and discovers a fundamentally new way in which the behavior of ions with the air-water interfaces should be probed. In Chapter 1, we introduce the motivation and methods and the overall structure of this thesis. Chapter 2 focuses on how MD simulations connect the statistical mechanics theory with the experimental observations. Chapter 3 discusses the simulation results revealing that the spreading of a droplet on a nanopillared graphene surface is driven by a pinned contact line and bending liquid-surface dynamics. Chapter 4 probes the interactions between a water drop and a holey graphene membrane, which is prepared by removing carbon atoms in a circular shape and which can serve as catalyst carriers. Accordingly, chapter 5 studies the effects of various terminations on water-holey graphene interactions, showing that water flows faster and more thoroughly through the membrane with hydrophobic terminations, compared to that with hydrophilic terminations. In chapter 6, simulations describe the generation of enhanced water-graphene surface area during the water-holey-graphene interactions in presence of an applied time-varying force on the water drop. In chapter 7, we focus on the ion-water interaction at the water-air interface to fully understand the fluidic dynamics during any seawater desalination. Our research revisits the energetic change while ion approaches water-air interface and shows that the presence of ion at the interface enhances capillary-wave fluctuation. Finally, in chapter 8 we summarize the main findings of the thesis and provide the scope of future research.Item Examining the role of water and hydrophobicity in folding, aggregation, and allostery(2018) Custer, Gregory Scott; Matysiak, Silvina; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Solvation and hydrophobicity drive many critical processes in nature, playing an important role in the folding of proteins, aggregation of surfactants into micelles, and in the disorder to order transitions that occur in some allosteric proteins upon ligand binding. Understanding how solvation and hydrophobicity affect these processes at a molecular level is important to finding new ways to use these processes, but it can be difficult to characterize these molecular details using experimental methods. Molecular dynamics (MD) simulations have proven useful in exploring details and thermodynamic conditions inaccessible in experiment, as MD captures the time evolution of the system at a molecular level. The phenomena which can be studied with an MD simulation depend on the mathematical model employed. Atomistic models provide the most detail for a simulation, but due to the computational costs required are not typically used to study phenomena which require large systems and time scales greater than several μs. Coarse-grained (CG) models reduce the complexity of the system being studied, enabling the exploration of phenomena that occur at longer time scales. We have developed CG models to study protein folding and surfactant aggregation. Our CG surfactant model uses a three-body potential to account for hydrogen bonding without an explicit electrostatic potential, reducing the computational cost of the model. With our surfactant model we studied the stability of non-ionic micelles at extremes of temperature, capturing a window of thermal stability with destabilization of the micelles at both high and low temperatures. We observed changes in structure and solvation of the micelle at low temperatures, with a shift in enthalpy of solvation water providing the driving force for destabilization. Solvation and hydrophobicity are also critical in the folding and stability of proteins. With a modified version of our surfactant model we characterized the folding landscape of a designed sequence which folds to a helical bundle in water. We found two competing folded states which differ by rotation of a helix and trade between hydrophobic packing and solvation of protein's core. Changes in hydrophobic packing can also be involved in the disorder to order transitions that occur upon liganding binding in an allosteric protein, such as the E. Coli biotin ligase/repressor (BirA), in which ligand binding promotes dimerization. We have used atomistic simulations of BirA mutants in collaboration with an experimental group to identify structural changes, accompanied by changes in solvation, at both the dimer interface and ligand binding regions for distal mutations which impact the functionality of BirA.Item Optical and quantum interferences in strong field ionization and optimal control(2017) Foote, David B.; Hill, Wendell T.; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)For decades, ultrafast laser pulses have been used to probe and control strong-field molecular dynamics, including in optimal control experiments. While these experiments successfully recover the optimal control pulses (OCPs), they have a limitation -- it is generally unknown how the OCP guides the target system to its final state. This thesis is concerned with "unpacking" OCPs to explain how they achieve their control goals. The OCPs that inspired this work consisted of pulse trains; a twin-peaked pulse (TPP) is the simplest example. Consequently, TPPs with variable interpeak delay and relative phase were employed in this work to study ionization, the first step in many control experiments. Two types of interference influence ionization from a TPP: optical interference (OI) between the electric fields of the two peaks, and quantum interference (QuI) between the electron wavepackets produced by the two peaks. Two sets of experiments were performed to determine what roles OI and QuI play in controlling ionization from a TPP and how they in turn influence subsequent molecular dynamics. The first set of experiments measured the total ionization yield induced by the TPPs. It was found that OI was principally responsible for changing the ion yield; QuI-induced oscillations were not observed. Small imperfections in the shape of the TPP (i.e., pedestals and subordinate peaks) were found to have a surprisingly large influence in the OI, highlighting the need for researchers in molecular control experiments to characterize the temporal profile of their pulses accurately. A time-dependent perturbation theory simulation showed that the signatures of QuI in the ionic continuum vanish when measuring {\it total} electron yield, but appear in {\it energy-resolved} electron yields. The second set of experiments measured photoelectron energy distributions from a TPP with a velocity map imager to search for QuI. The experiments were performed at high intensities (~10^14 W/cm^2) where the ponderomotive energy tends to wash out the fine energy structures of QuI. The thesis ends by proposing a modified, low-intensity experiment that will allow for the first unambiguous observation of QuI in non-resonant, multiphoton ionization.Item UNDERSTANDING THE MOTILITY OF MOLECULAR MOTORS USING THEORY AND SIMULATIONS(2017) Goldtzvik, Yonathan Yitshak; Thirumalai, Devarajan; Biophysics (BIPH); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Molecular motors are indispensable machines that are in charge of transporting cargoes within living cells. Despite recent advances in the study of these molecules, there is much that we still do not understand regarding the underlying mechanisms that allow them to efficiently move cargoes along polar cellular filaments. In this thesis, I report my investigation on two motor proteins superfamilies, dyneins and kinesins. Using theoretical modeling, we provide fundamental insight into their function. Dynein is a large motor that transports cargo along microtubules towards their negative pole. Unlike other motors, such as conventional kinesin, the motility of dynein is highly stochastic. We developed a novel theoretical approach, which reproduces a wide variety of its properties, including the unique step size distribution observed in experiments. Furthermore, our model enables us to derive several simple expressions that can be fitted to experiment, thus providing a physical interpretation. A less understood aspect of dynein is the complex set of allosteric transitions in response to ATP binding and hydrolysis, and microtubule binding. The resulting conformational transitions propel the motor forward to the minus end of the microtubule. Furthermore, its activity is regulated by external strain. Using coarse grained Brownian dynamics simulations, we show that a couple of insert loops in the AAA2, a sub domain in the AAA+ ring in the motor domain, play an important role in several of the alllosteric pathways. Kinesins are highly processive motor proteins that transport cargo along microtubules toward their positive poles. Experiments show that the kinesin motor domains propel the motor forward by passing each other in a hand-over-hand motion. However, there is a debate as to whether the motor domains do so in a symmetrical manner or an asymmetrical motion. Using coarse grained Brownian dynamics simulations of the kinesin dimer, we show that the kinesin stepping mechanism is influenced by the size of its cargo. Furthermore, we find that stepping occurs by a combinations of both the symmetric and asymmetric mechanisms. The results I present in this thesis are a testimony that theoretical approaches are invaluable to the study of molecular motors.Item Feasibility of in vivo SAXS imaging for detection of Alzheimer's disease(2017) Choi, Mina; Chen, Yu; Badano, Aldo; Bioengineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Small-angle x-ray scattering (SAXS) imaging has been proposed as a technique to characterize and selectively image structures based on electron density structure which allows for discriminating materials based on their scatter cross sections. This dissertation explores the feasibility of SAXS imaging for the detection of Alzheimer's disease (AD) amyloid plaques. The inherent scatter cross sections of amyloid plaque serve as biomarkers in vivo without the need of injected molecular tags. SAXS imaging can also assist in a better understanding of how these biomarkers play a role in Alzheimer’s disease which in turn can lead to the development of more effective disease-modifying therapies. I implement simulations of x-ray transport using Monte Carlo methods for SAXS imaging enabling accurate calculation of radiation dose and image quality in SAXS-computed tomography (CT). I describe SAXS imaging phantoms with tissue-mimicking material and embedded scatter targets as a way of demonstrating the characteristics of SAXS imaging. I also performed a comprehensive study of scattering cross sections of brain tissue from measurements of ex-vivo sections of a wild-type mouse brain and reported generalized cross sections of gray matter, white matter, and corpus callosum obtained and registered by planar SAXS imaging. Finally, I demonstrate the ability of SAXS imaging to locate an amyloid fibril pellet within a brain section. This work contributes to novel application of SAXS imaging for Alzheimer's disease detection and studies its feasibility as an imaging tool for AD biomarkers.Item COLLISION DYNAMICS OF HIGHLY ORIENTED SUPER ROTOR MOLECULES FROM AN OPTICAL CENTRIFUGE(2017) Murray, Matthew J.; Mullin, Amy S; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Sophisticated optical methods provide some of the most promising tools for complete control of a molecule’s energy and orientation, which enables a more complete understanding of chemical reactivity and structure. This dissertation investigates the collision dynamics of molecular super rotors with oriented angular momentum prepared in an optical centrifuge. Molecules with anisotropic polarizabilities are trapped in the electric field of linearly polarized light and then angularly accelerated from 0 to 35 THz over the duration of the optical pulse. This process drives molecules to extreme rotational states and the ensemble of molecules has a unidirectional sense of rotation determined by the propagation of the optical field. High resolution transient IR absorption spectroscopy of the super rotor molecules reveals the dynamics of collisional energy transfer. These studies show that high energy CO2 and CO rotors release large amounts of translational energy through impulsive collisions. Time-evolution of the translational energy distribution of the CO2 J=0-100 state shows that depletion from low J states involves molecules with sub-thermal velocities. Polarization-dependent Doppler profiles of CO rotors show anisotropic kinetic energy release and reveal a majority population of molecular rotors in the initial plane of rotation. Experimental modifications improved signal to noise levels by a factor of 10, enabling new transient studies in the low-pressure, single-collision regime. Polarization-dependent studies show that CO2 rotors in the J=54-100 states retain their initial angular momentum orientation, and that this effect increases as a function of rotational angular momentum. These studies show that rotating molecules behave like classical gyroscopes. Polarization-dependent measurements of CO2 rotors in the presence of He and Ar buffer gases show that CO2 super rotors are more strongly relaxed by He collisions, demonstrating the importance of rotational adiabaticity in the relaxation process. Quantum scattering calculations of the He-CO2 and Ar-CO2 collision systems were performed to interpret the qualitative features of the experimental results. This work provides a detailed mechanistic understanding of the unique collisional dynamics of super rotor molecules.Item MODELING LIQUID EVAPORATION AND USING MOLECULAR DYNAMICS SIMULATION TO ESTIMATE DIFFUSION COEFFICIENTS AND RELATIVE SOLVENT DRYING TIMES(2017) Choudhary, Rehan; Klauda, Jeffery B; Chemical Engineering; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In this thesis, the Simultaneous Mass and Energy Evaporation (SM2E) model is presented. This model is based on theoretical expressions for mass and energy transfer and can be used to estimate evaporation rates for pure liquids as well as liquid mixtures at laminar, transition, and turbulent flow conditions. However, due to limited availability of evaporation data, the model has so far only been tested against data for pure liquids and binary mixtures. The model can take evaporative cooling into account. For the case of isothermal evaporation, the model becomes a mass transfer-only model. Also in this thesis, molecular dynamics (MD) simulation is used to estimate gas phase diffusion coefficients based on mean-square displacement methods and results are compared with Chapman-Enksog theory. MD simulation is also used to model evaporation of solvents into air and relative solvent drying times based on simulation are compared with measured values.